Quick's Hole is a narrow passage that lies between the islands of Pasque and Nashawena, a treacherous passage lined with boulders on either side that earned its name from the swift currents running through it.

The hole lies seven miles northwest of Menemsha. Vessels traveling between Menemsha and New Bedford use this channel to thread the chain of the Elizabeth Islands. Rocks are visible along the shoreline, and many more dangers lie below, charted and uncharted.

On Tuesday afternoon the Thomas Jefferson, a 208-foot research and survey vessel used by the National Oceanic and Atmospheric Administration (NOAA) for ocean research, was anchored off Cape Pogue. The ship was off the Vineyard for a final day as work was completed on a survey of the waters of Edgartown, Cow Bay and parts of Nantucket Sound.

Earlier this summer the Thomas Jefferson was in Quick's Hole as the ship's crew and supporting vessels did extensive survey work in the waters around the Vineyard. While the intention was to update existing navigational maps, the Thomas Jefferson also found three wrecked fishing boats and a sunken barge.

It has been a busy summer for the ship, one of a fleet of 17 white-hulled research and survey vessels used by NOAA. The ship's principal purpose is to conduct hydrographic surveys for updating nautical maps, and it is loaded with an array of state-of-the-art equipment capable of detecting just about anything below. Scientists on board have more than just experience to plot maps; they can find sunken ships and lost airplanes at just about any depth.

On board the Thomas Jefferson, executive officer Shepard M. Smith, 35, has an unusual job. The ship is a floating science center, with staff and crew of varying expertise.

Plenty of areas along the coast haven't been surveyed in more than 70 years. The work of the ship is ongoing, with no shortage of assignments - only a shortage of time and resources. The Thomas Jefferson came to the Vineyard this summer at the request of the U.S. Coast Guard to update two critical areas for passage: Quick's Hole and Edgartown harbor.

The survey of the Edgartown harbor was driven in part by Capt. Daniel Farren, who pilots the passenger ferry Pied Piper between Falmouth and Edgartown. Captain Farren wants a shorter and safer route, and Mr. Smith explained that there is an area of rocks and a buoy outside of Edgartown harbor that all big vessels pass around.

Sailboats and powerboats leaving or coming into Edgartown harbor must pass around the red buoy which lies three miles north of the Edgartown Lighthouse in Nantucket Sound. A number of rocks appear on the charts just south of the buoy. Some have names: Allen Rock, Hatsett Rock and Monohansett Rock. The water depth on old charts ranges from two to 12 feet.

The survey work is done using a 29-foot aluminum diesel-powered launch. The vessel has a sonar sighting device on the bottom.

Operations officer Marc Moser described the bottom of Edgartown harbor as little more than shifting sand and a few rocks. "It is not very exciting," he said.

Quick's Hole is an entirely different place, a place with a diverse underwater landscape. "Quick's Hole is spectacular," Mr. Smith said. With the help of senior survey technician Peter Lewit Mr. Smith called a huge computer file onto the screen that depicted the passage in three dimensions. With the click of a mouse, Mr. Smith sped through an area of bottom to a sunken fishing boat lying on the sand. The wrecked boat lay near some hills and a few valleys, partially buried. Lobster pots or fish pots could be seen piled up in the sand just to stern of the vessel.

Mr. Lewit said it is likely that when the boat sank the lobster gear fell to stern. No one aboard knew how the vessel sank.

North of Quick's Hole, Mr. Smith clicked his mouse and displayed what appeared to be an upside down barge.

Then he showed a place on the sandy bottom where an anchor dragged a deep trench.

Larry Poppe, who works for the United States Geodetic Survey in Woods Hole, stepped over to look at the screen. He said the value of the information gathered goes well beyond navigational maps and identifying shipwrecks. "We can interpret the distribution of sedimentary environments and fish habitat. This information is of great interest to state agencies like Massachusetts Coastal Zone Management and fisheries people."

He pointed to an area of the bottom where strands of elevated sand looked like small mountain ranges and valleys. The mountains and valleys were created by strong currents in Vineyard Sound.

Mr. Poppe said the survey might be used to help fisheries managers determine how heavy fishing gear impacts the bottom. This could help identify ideal and less-than-ideal lobster habitat.

Mr. Smith said that when NOAA resurveys areas, scientists will be able to see and make note of any changes. For instance, he said, they might be able to report how long it takes the ocean to recover after heavy fishing gear has been dragged along the bottom.

In the large computer room, Capt. Emily B. Christman stepped in to watch. The captain of the ship had concerns beyond the survey work. "I spend most of my time worrying about the weather," she said. There are 33 people aboard the Thomas Jefferson plus plenty of equipment. The captain credited other captains for their help. "I especially appreciate how much cooperation we have gotten from the ferries and other vessels," she said.

Mr. Smith said NOAA has created a priority system for determining what areas along the coast get surveyed. He said at least half the country's navigable coast has not been surveyed since the advent of sonar. Lead lines - weighted lines with a piece of lead at the bottom - were used before the 1940s to measure depth. "We still use lead lines to check ourselves," Mr. Smith said.

Changes in traffic and need determine where the maps are updated. Safety concerns for seagoing vessels drive much of the survey work.

Mr. Smith said cruise ships and merchant ships are getting larger, and he said a rising number of coastal freighters can be found at sea.

Large ships draw more water than they did years ago; hence new attention is paid to the bottom.

In the summer of 1992 the Queen Elizabeth II ran aground in Vineyard Sound, a few miles south of Cuttyhunk. Vineyard Sound had not seen many cruise ships, and suddenly there was new interest. NOAA was sued by the Cunard Line over the grounding, because the rocks that tore a huge hole in the ship weren't on the charts, Mr. Smith said. Coincidentally, in that same year, he said NOAA was engaged in a survey of the approach to Buzzards Bay. "That rock that was hit by the QEII was always there, we just hadn't seen it," Mr. Smith said.

The rock, surrounded by paint chips, was later found by the NOAA sister ship Rudy.

The equipment on the Thomas Jefferson is top of the line. One five-foot-long sonar "fish" that the ship tows is valued at a quarter million dollars. Two kinds of sonar are employed in the study of the bottom. There is side scan sonar, which has a high resolution and can spot very small objects. "It was used in the search for TWA 800," Mr. Smith said, referring to the plane crash far offshore on July 17, 1996. He said the sonar was able to spot a coffee urn in the debris field of the crash.

A newer version of scanning the bottom is done with the multi-beam echo sounder, a device that is more precise in shallow water.

The equipment aboard the Thomas Jefferson was the same equipment used by the ship Rudy when it went looking for the Piper Saratoga II flown by John F. Kennedy Jr. that crashed south of the Vineyard in July of 1999.

Mr. Smith said the ship is ready at a moment's notice for assignments that go beyond the primary role of updating navigational maps. "In just the time it takes to steam, we can be ready to go anywhere," he said. There are four divers aboard.

On Tuesday, Captain Christman fretted about the approach of poor weather from Hurricane Jeanne. Rain and fog surrounded the ship as she steamed away from Edgartown to spend the night out of the storm's way, in Tarpaulin Cove. The ship's mission for the moment in Vineyard waters was done.